Align Inositol transport system permease protein (characterized)
to candidate 3607106 Dshi_0528 Monosaccharide-transporting ATPase (RefSeq)
Query= reanno::WCS417:GFF2333 (340 letters) >FitnessBrowser__Dino:3607106 Length = 334 Score = 172 bits (437), Expect = 8e-48 Identities = 107/313 (34%), Positives = 175/313 (55%), Gaps = 12/313 (3%) Query: 27 FLVLIGIGLVFELFGWIVRDQSFLMNSQRLVLMILQVSIIGLLAIGVTQVIITTGIDLSS 86 F +LI + VF L + D+ ++SQ L M Q +LA+ +T ++T GIDLS Sbjct: 14 FRLLIIMVFVFGLMSVLSPDR--FLSSQNLTSMAFQFPEFAILALAMTIAMMTGGIDLSV 71 Query: 87 GSVLALSAMIAASLAQTSDFSRAVFPSLTDLPVWIPVAM--GLGVGLLAGAINGSIIAVT 144 + LSA++AA + + FS A P+ +W+ +A+ L +G +AG INGS++A Sbjct: 72 VGIANLSAVVAALIL--THFSNAEMPAAQSA-IWLAIAITAALCIGAIAGLINGSLVAFF 128 Query: 145 GIPPFIATLGMMVSARGLARYYTEGQPVSMLSDSYTAIGHGAM-----PVIIFLVVAVIF 199 G+PP +ATLG + G A T G V D+ IG+ + P+I+F V+A + Sbjct: 129 GLPPILATLGSGLVFTGFAIAMTGGSAVMGFPDTVALIGNATLAGVPVPLILFAVLAFLL 188 Query: 200 HIALRYTKYGKYTYAIGGNMQAARTSGINVKRHLIIVYSIAGLLAGLAGVVASARAATGQ 259 H+ L T +G G N AA + I++ R L+ VY IAG+ A +AG++ +RA + + Sbjct: 189 HLVLTRTAFGLRVTMYGANPLAALYAAIDINRMLLKVYVIAGMFASVAGLIIMSRANSAK 248 Query: 260 AGMGMSYELDAIAAAVIGGTSLAGGVGRITGTVIGALILGVMASGFTFVGVDAYIQDIIK 319 A G SY L A+ AV+GG + GG GR+ G V+ L + ++SG +GV + +++I Sbjct: 249 ADYGSSYLLLAVLIAVLGGVNPYGGYGRVIGVVLAVLSMQFLSSGLNMLGVSNFARELIW 308 Query: 320 GLIIVVAVVIDQY 332 G ++++ +VI+ + Sbjct: 309 GALLILVMVINTH 321 Lambda K H 0.325 0.140 0.394 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 230 Number of extensions: 12 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 340 Length of database: 334 Length adjustment: 28 Effective length of query: 312 Effective length of database: 306 Effective search space: 95472 Effective search space used: 95472 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory